4gd6 - Revision history

OCA at 06:48, 26 October 2022

2022-10-26T06:48:45Z

←Older revision		Revision as of 06:48, 26 October 2022
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	==SHV-1 beta-lactamase in complex with penam sulfone SA1-204==		==SHV-1 beta-lactamase in complex with penam sulfone SA1-204==
-	<StructureSection load='4gd6' size='340' side='right' caption='[[4gd6]], [[Resolution\|resolution]] 1.53Å' scene=''>	+	<StructureSection load='4gd6' size='340' side='right'caption='[[4gd6]], [[Resolution\|resolution]] 1.53Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4gd6]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~"bacillus_pneumoniae"_(schroeter_1886)_flugge_1886 "bacillus~~ pneumoniae~~" (schroeter 1886) flugge 1886~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4GD6 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4GD6 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4gd6]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Klebsiella_pneumoniae Klebsiella pneumoniae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4GD6 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4GD6 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=17K:(3R)-N-(2-FORMYLINDOLIZIN-3-YL)-4-[(PHENYLACETYL)OXY]-3-SULFINO-D-VALINE'>17K</scene>, <scene name='pdbligand=MA4:CYCLOHEXYL-HEXYL-BETA-D-MALTOSIDE'>MA4</scene~~></td></tr>~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=17K:(3R)-N-(2-FORMYLINDOLIZIN-3-YL)-4-[(PHENYLACETYL)OXY]-3-SULFINO-D-VALINE'>17K</scene>, <scene name='pdbligand=MA4:CYCLOHEXYL-HEXYL-BETA-D-MALTOSIDE'>MA4</scene></td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3d4f\|3d4f]], [[4gd8\|4gd8]], [[4gdb\|4gdb]]</td></tr>~~	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=4gd6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4gd6 OCA], [https://pdbe.org/4gd6 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4gd6 RCSB], [https://www.ebi.ac.uk/pdbsum/4gd6 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4gd6 ProSAT]</span></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">bla, shv1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=573 "Bacillus pneumoniae" (Schroeter 1886) Flugge 1886])</td></tr>	+
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Beta-lactamase Beta-lactamase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.2.6 3.5.2.6] </span></td></tr>	+
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4gd6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4gd6 OCA], [~~http~~://pdbe.org/4gd6 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4gd6 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4gd6 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4gd6 ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/BLA1_KLEPN BLA1_KLEPN]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 19:		Line 18:
	</div>		</div>
	<div class="pdbe-citations 4gd6" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 4gd6" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Beta-lactamase 3D structures\|Beta-lactamase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Beta-lactamase~~]]	+	[[Category: Klebsiella pneumoniae]]
-	[[Category: ~~Akker, F van den~~]]	+	[[Category: Large Structures]]
-	[[Category: Wei, K]]	+	[[Category: Wei K]]
-	[[Category: ~~Class a beta-lactamase]]~~	+	[[Category: Van den Akker F]]
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: Hydrolase-hydrolase inhibitor complex~~]]	+

OCA at 08:27, 15 November 2017

2017-11-15T08:27:30Z

←Older revision		Revision as of 08:27, 15 November 2017
Line 19:		Line 19:
	</div>		</div>
	<div class="pdbe-citations 4gd6" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 4gd6" style="background-color:#fffaf0;"></div>
-
-	==See Also==
-	*[[Beta-lactamase\|Beta-lactamase]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 17:20, 4 August 2016

2016-08-04T17:20:40Z

←Older revision		Revision as of 17:20, 4 August 2016
Line 1:		Line 1:
		+
	==SHV-1 beta-lactamase in complex with penam sulfone SA1-204==		==SHV-1 beta-lactamase in complex with penam sulfone SA1-204==
	<StructureSection load='4gd6' size='340' side='right' caption='[[4gd6]], [[Resolution\|resolution]] 1.53Å' scene=''>		<StructureSection load='4gd6' size='340' side='right' caption='[[4gd6]], [[Resolution\|resolution]] 1.53Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4gd6]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Klebsiella_pneumoniae Klebsiella~~ pneumoniae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4GD6 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4GD6 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4gd6]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_pneumoniae"_(schroeter_1886)_flugge_1886 "bacillus pneumoniae" (schroeter 1886) flugge 1886]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4GD6 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4GD6 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=17K:(3R)-N-(2-FORMYLINDOLIZIN-3-YL)-4-[(PHENYLACETYL)OXY]-3-SULFINO-D-VALINE'>17K</scene>, <scene name='pdbligand=MA4:CYCLOHEXYL-HEXYL-BETA-D-MALTOSIDE'>MA4</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=17K:(3R)-N-(2-FORMYLINDOLIZIN-3-YL)-4-[(PHENYLACETYL)OXY]-3-SULFINO-D-VALINE'>17K</scene>, <scene name='pdbligand=MA4:CYCLOHEXYL-HEXYL-BETA-D-MALTOSIDE'>MA4</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3d4f\|3d4f]], [[4gd8\|4gd8]], [[4gdb\|4gdb]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3d4f\|3d4f]], [[4gd8\|4gd8]], [[4gdb\|4gdb]]</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">bla, shv1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=573 ~~Klebsiella~~ pneumoniae])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">bla, shv1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=573 "Bacillus pneumoniae" (Schroeter 1886) Flugge 1886])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Beta-lactamase Beta-lactamase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.2.6 3.5.2.6] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Beta-lactamase Beta-lactamase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.2.6 3.5.2.6] </span></td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4gd6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4gd6 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4gd6 RCSB], [http://www.ebi.ac.uk/pdbsum/4gd6 PDBsum]</span></td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4gd6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4gd6 OCA], [http://pdbe.org/4gd6 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4gd6 RCSB], [http://www.ebi.ac.uk/pdbsum/4gd6 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4gd6 ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 17:		Line 18:
	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	</div>		</div>
		+	<div class="pdbe-citations 4gd6" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 25:		Line 27:
	</StructureSection>		</StructureSection>
	[[Category: Beta-lactamase]]		[[Category: Beta-lactamase]]
-	[[Category: Klebsiella pneumoniae]]
	[[Category: Akker, F van den]]		[[Category: Akker, F van den]]
	[[Category: Wei, K]]		[[Category: Wei, K]]

OCA at 11:12, 21 December 2014

2014-12-21T11:12:24Z

←Older revision		Revision as of 11:12, 21 December 2014
Line 1:		Line 1:
-	~~{{STRUCTURE_4gd6\| PDB=4gd6 \| SCENE= }}~~	+	==SHV-1 beta-lactamase in complex with penam sulfone SA1-204==
-	===SHV-1 beta-lactamase in complex with penam sulfone SA1-204===	+	<StructureSection load='4gd6' size='340' side='right' caption='[[4gd6]], [[Resolution\|resolution]] 1.53Å' scene=''>
-	~~{{ABSTRACT_PUBMED_23145056}}~~	+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[4gd6]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Klebsiella_pneumoniae Klebsiella pneumoniae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4GD6 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4GD6 FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=17K:(3R)-N-(2-FORMYLINDOLIZIN-3-YL)-4-[(PHENYLACETYL)OXY]-3-SULFINO-D-VALINE'>17K</scene>, <scene name='pdbligand=MA4:CYCLOHEXYL-HEXYL-BETA-D-MALTOSIDE'>MA4</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3d4f\|3d4f]], [[4gd8\|4gd8]], [[4gdb\|4gdb]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">bla, shv1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=573 Klebsiella pneumoniae])</td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Beta-lactamase Beta-lactamase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.2.6 3.5.2.6] </span></td></tr>
		+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4gd6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4gd6 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4gd6 RCSB], [http://www.ebi.ac.uk/pdbsum/4gd6 PDBsum]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Bacterial beta-lactamase enzymes are in large part responsible for the decreased ability of beta-lactam antibiotics to combat infections. The inability to overcome beta-lactamase mediated resistance spurred the development of inhibitors with penems and penam sulfones being amongst the most potent and broad spectrum mechanism-based inactivators. These inhibitors form covalent, "suicide-type" inhibitory intermediates that are attached to the catalytic S70 residue. To further probe the details of the mechanism of beta-lactamase inhibition by these novel compounds, we determined the crystal structures of SHV-1 bound with penem 1, and penam sulfones SA1-204 and SA3-53. Comparison with each other and with previously determined crystal structures of members of these classes of inhibitors suggests that the final conformation of the covalent adduct can vary greatly amongst the complex structures. In contrast, a common theme of carbonyl conjugation as a mechanism to avoid deacylation emerges despite that the penem and penam sulfone inhibitors form different types of intermediates. The detailed insights gained from this study could be used to further improve new mechanism-based inhibitors of these common class A serine beta-lactamases.

-	~~==About this Structure==~~	+	Structures of SHV-1 beta-lactamase with penem and penam sulfone inhibitors that form cyclic intermediates stabilized by carbonyl conjugation.,Ke W, Pattanaik P, Bethel CR, Sheri A, Buynak JD, Bonomo RA, van den Akker F PLoS One. 2012;7(11):e49035. doi: 10.1371/journal.pone.0049035. Epub 2012 Nov 8. PMID:23145056<ref>PMID:23145056</ref>
-	~~[[4gd6]] is a~~ 1 ~~chain structure~~ with ~~sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Klebsiella_pneumoniae Klebsiella pneumoniae]~~. ~~Full crystallographic information is available from [http~~:/~~/oca~~.~~weizmann~~.ac.il/~~oca-bin/ocashort?id=4GD6 OCA].~~	+

-	==~~Reference~~==	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~<ref group~~=~~"xtra">PMID:023145056</ref>~~<references ~~group="xtra"~~/><~~references~~/>	+	</div>
		+
		+	==See Also==
		+	*[[Beta-lactamase\|Beta-lactamase]]
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
	[[Category: Beta-lactamase]]		[[Category: Beta-lactamase]]
	[[Category: Klebsiella pneumoniae]]		[[Category: Klebsiella pneumoniae]]
-	[[Category: Akker, F van den.]]	+	[[Category: Akker, F van den]]
-	[[Category: Wei, K.]]	+	[[Category: Wei, K]]
	[[Category: Class a beta-lactamase]]		[[Category: Class a beta-lactamase]]
	[[Category: Hydrolase]]		[[Category: Hydrolase]]
	[[Category: Hydrolase-hydrolase inhibitor complex]]		[[Category: Hydrolase-hydrolase inhibitor complex]]

OCA at 05:16, 1 August 2013

2013-08-01T05:16:12Z

←Older revision		Revision as of 05:16, 1 August 2013
Line 1:		Line 1:
-	~~'''Unreleased structure'''~~	+	{{STRUCTURE_4gd6\| PDB=4gd6 \| SCENE= }}
		+	===SHV-1 beta-lactamase in complex with penam sulfone SA1-204===
		+	{{ABSTRACT_PUBMED_23145056}}

-	~~The entry~~ 4gd6 is ~~ON HOLD until Jul 31 2014~~	+	==About this Structure==
		+	[[4gd6]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Klebsiella_pneumoniae Klebsiella pneumoniae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4GD6 OCA].

-	~~Authors~~: ~~van den~~ Akker, F., Wei, K.	+	==Reference==
-		+	<ref group="xtra">PMID:023145056</ref><references group="xtra"/><references/>
-	~~Description~~: ~~SHV-1~~ beta-lactamase ~~in complex with penam sulfone SA1~~-~~204~~	+	[[Category: Beta-lactamase]]
		+	[[Category: Klebsiella pneumoniae]]
		+	[[Category: Akker, F van den.]]
		+	[[Category: Wei, K.]]
		+	[[Category: Class a beta-lactamase]]
		+	[[Category: Hydrolase]]
		+	[[Category: Hydrolase-hydrolase inhibitor complex]]

OCA at 14:48, 10 July 2013

2013-07-10T14:48:13Z

←Older revision		Revision as of 14:48, 10 July 2013
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 4gd6 is ON HOLD until ~~Paper Publication~~	+	The entry 4gd6 is ON HOLD until Jul 31 2014

	Authors: van den Akker, F., Wei, K.		Authors: van den Akker, F., Wei, K.

	Description: SHV-1 beta-lactamase in complex with penam sulfone SA1-204		Description: SHV-1 beta-lactamase in complex with penam sulfone SA1-204

OCA at 09:00, 21 November 2012

2012-11-21T09:00:14Z

←Older revision		Revision as of 09:00, 21 November 2012
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 4gd6 is ON HOLD	+	The entry 4gd6 is ON HOLD until Paper Publication

	Authors: van den Akker, F., Wei, K.		Authors: van den Akker, F., Wei, K.

	Description: SHV-1 beta-lactamase in complex with penam sulfone SA1-204		Description: SHV-1 beta-lactamase in complex with penam sulfone SA1-204

OCA at 13:18, 8 November 2012

2012-11-08T13:18:01Z

←Older revision		Revision as of 13:18, 8 November 2012
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 4gd6 is ON HOLD ~~until sometime in the future~~	+	The entry 4gd6 is ON HOLD

	Authors: van den Akker, F., Wei, K.		Authors: van den Akker, F., Wei, K.

	Description: SHV-1 beta-lactamase in complex with penam sulfone SA1-204		Description: SHV-1 beta-lactamase in complex with penam sulfone SA1-204

OCA at 05:33, 22 August 2012

2012-08-22T05:33:09Z

←Older revision		Revision as of 05:33, 22 August 2012
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 4gd6 is ON HOLD	+	The entry 4gd6 is ON HOLD until sometime in the future

	Authors: van den Akker, F., Wei, K.		Authors: van den Akker, F., Wei, K.

	Description: SHV-1 beta-lactamase in complex with penam sulfone SA1-204		Description: SHV-1 beta-lactamase in complex with penam sulfone SA1-204

OCA: Protected "4gd6" [edit=sysop:move=sysop]

2012-08-08T05:01:01Z

Protected "4gd6" [edit=sysop:move=sysop]

←Older revision

Revision as of 05:01, 8 August 2012